GREMLIN Database
RPOZ - DNA-directed RNA polymerase subunit omega
UniProt: P0A800 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10899
Length: 91 (79)
Sequences: 440 (223)
Seq/√Len: 25.0

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_L58_L5.7951.00
41_E49_I4.3321.00
39_V49_I3.1171.00
13_I22_V2.9461.00
9_A55_E2.4070.98
9_A14_G2.2740.98
10_V14_G2.0020.95
12_K57_G1.8870.93
17_F28_R1.8610.93
77_A80_L1.7220.89
22_V64_L1.6340.87
7_Q31_Q1.5310.83
76_E79_E1.5250.82
15_N28_R1.3830.76
75_Q79_E1.3770.75
16_R50_A1.3480.74
18_D78_A1.3470.74
75_Q78_A1.3450.74
6_V15_N1.3340.73
18_D23_A1.2600.69
38_L59_I1.2470.68
16_R52_R1.2270.66
14_G55_E1.1460.61
30_M41_E1.1250.60
29_Q65_D1.1110.59
62_Q66_V1.1020.58
40_P62_Q1.0850.57
22_V62_Q1.0540.55
76_E80_L1.0480.54
37_P47_T1.0260.53
12_K21_L1.0250.52
4_V48_V1.0190.52
22_V61_N1.0190.52
4_V10_V1.0140.52
8_D34_G0.9920.50
72_Q75_Q0.9860.50
4_V25_R0.9850.50
11_E76_E0.9780.49
31_Q46_T0.9780.49
59_I63_I0.9670.48
28_R31_Q0.9590.48
47_T58_L0.9530.47
14_G47_T0.9450.47
17_F24_A0.9370.46
68_E71_E0.9290.46
13_I19_L0.9280.45
16_R28_R0.9240.45
67_R72_Q0.9100.44
44_D47_T0.9040.44
34_G69_R0.8840.42
12_K24_A0.8480.40
20_V69_R0.8470.40
40_P43_N0.8470.40
11_E14_G0.8440.40
29_Q71_E0.8360.39
25_R29_Q0.8280.38
48_V55_E0.8220.38
63_I66_V0.8210.38
36_D80_L0.8090.37
11_E61_N0.7940.36
66_V69_R0.7850.35
21_L57_G0.7850.35
40_P49_I0.7610.34
25_R65_D0.7580.34
22_V35_K0.7580.34
70_Q76_E0.7580.34
21_L27_A0.7440.33
8_D48_V0.7330.32
9_A18_D0.7240.32
29_Q39_V0.7200.31
33_G80_L0.7110.31
8_D55_E0.7100.31
25_R68_E0.7060.30
37_P49_I0.7030.30
73_Q80_L0.7020.30
46_T50_A0.7000.30
15_N52_R0.6960.30
61_N66_V0.6940.30
50_A54_I0.6930.30
14_G24_A0.6900.29
7_Q60_N0.6880.29
12_K25_R0.6840.29
21_L25_R0.6790.29
35_K50_A0.6750.29
38_L57_G0.6610.28
61_N64_L0.6600.28
55_E58_L0.6600.28
63_I67_R0.6540.27
13_I36_D0.6530.27
4_V67_R0.6330.26
30_M37_P0.6330.26
16_R24_A0.6320.26
12_K72_Q0.6260.26
7_Q34_G0.6250.26
24_A42_E0.6130.25
63_I70_Q0.6110.25
4_V78_A0.5960.24
22_V74_E0.5950.24
30_M34_G0.5950.24
14_G20_V0.5910.24
20_V40_P0.5910.24
36_D78_A0.5830.23
27_A56_E0.5730.23
25_R59_I0.5620.22
66_V73_Q0.5500.22
75_Q80_L0.5480.22
70_Q75_Q0.5380.21
30_M77_A0.5320.21
21_L45_K0.5210.20
21_L47_T0.5180.20
10_V29_Q0.5170.20
46_T59_I0.5140.20
20_V34_G0.5120.20
39_V77_A0.5060.20
20_V55_E0.5040.20
67_R71_E0.5040.20
29_Q37_P0.5030.20
36_D74_E0.5000.19
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
4yfkE 1 0.978 99.9 0.334 Contact Map
2a6hE 1 0.8791 99.8 0.467 Contact Map
4aybK 1 0.8571 99.7 0.492 Contact Map
4qiwK 1 0.6044 99.6 0.563 Contact Map
1qklA 1 0.9121 99.6 0.565 Contact Map
3h0gF 1 0.8791 99.5 0.57 Contact Map
1twfF 1 0.8901 99.4 0.593 Contact Map
4w20r 1 0.4286 8.3 0.932 Contact Map
3nuhB 1 0.1319 8.2 0.932 Contact Map
4qmfD 1 0.3407 3.5 0.943 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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